Atom Nomenclature for LK2

The atom nomenclature in PDB data files was revised with the release of data in the PDB Format Version 3.0. These changes make the PDB atom names used by PDB compliant with existing IUPAC nomenclature for standard amino acid and nucleotides (Pure & Appl. Chem., 70, 117-142, 1998) with the exception of the well established convention for C-terminal atoms OXT and HXT. A small number of additional changes were introduced in Version 3 to make atom labeling more conventional. The following chemical diagrams and tables provide the correspondences between atom names used in Version 3 and Version 2 PDB formats.

Labeled Chemical Diagrams

Chemical diagram with format V3 atom labels (heavy atoms)
Chemical diagram with format V3 atom labels (all atoms)
Chemical diagram with format V2 atom labels (heavy atoms)
Chemical diagram with format V2 atom labels (all atoms)

Atom Name Correspondences for LK2

Atom Name (V3) Atom Name (V2)
O32 O32
S11 S11
O33 O33
N N
CA CA
C C
O O
OXT OXT
CB CB
CG CG
CD CD
OE2 OE2
OE1 OE1
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
C21 C21
C20 C20
C19 C19
C18 C18
O22 O22
C23 C23
C24 C24
C29 C29
C44 C44
H H
HA HA
HBC1 1HBC
HBC2 2HBC
HXT HXT
HGC1 1HGC
HGC2 2HGC
HE2 HE2
H13 H13
H17 H17
H14 H14
H21 H21
H18 H18
H19 H19
H231 1H23
H232 2H23
H241 1H24
H242 2H24
H291 1H29
H292 2H29
H441 1H44
H442 2H44
H443 3H44